I want to include the AGR in my product, but not pick up all the other
TPTP software (adding extra menus and perspectives etc). Is there a
minimal feature set I can include when packaging my product with PDE?

but I have some errors reported by PDE, such as.
While loading class "org.eclipse.hyades.ui.internal.util.ImageManager",
thread "main" timed out waiting (5000ms) for thread "Worker-3" to finish
starting bundle "org.eclipse.hyades.ui". To avoid deadlock, thread "main"

I also note imports such as org.apache.fop.* are not properly resolved.